RNA category is based on mRNA expression levels in the analyzed samples (RNA assay description). The categories include: tissue/cell line enriched, group enriched, tissue/cell line enhanced, expressed in all, mixed and not detected. RNA category is calculated separately for The Cancer Genome Atlas (TCGA) data from cancer tissues and internally generated Human Protein Atlas (HPA) data from normal tissues and cell lines.
TCGA (cancer tissue):
Expressed in all
HPA (cell line):
Cell line enhanced (Daudi, REH)
HPA (normal tissue):
Protein evidence scores are generated from several independent sources and are classified as evidence at i) protein level, ii) transcript level, iii) no evidence, or iv) not available.
Evidence at protein level
Protein expression normal tissuei
A summary of the overall protein expression pattern across the analyzed normal tissues. The summary is based on knowledge-based annotation.
"Estimation of protein expression could not be performed. View primary data." is shown for genes analyzed with a knowledge-based approach where available RNA-seq and gene/protein characterization data has been evaluated as not sufficient in combination with immunohistochemistry data to yield a reliable estimation of the protein expression profile.
Nuclear and cytoplasmic expression in several tissues, most abundant in leukocytes.
ANTIBODY IHC RELIABILITY
Data reliability descriptioni
Standardized explanatory sentences with additional information required for full understanding of the knowledge-based expression profile.
Antibody staining mainly consistent with RNA expression data. Presumed off target binding observed and disregarded.
Reliability score (score description), divided into Supported, Approved, or Uncertain, is evaluated in normal tissues and based on consistency between the staining pattern of one antibody or several antibodies with RNA-seq data and available gene/protein characterization data.
Kaplan-Meier plots for all cancers where high expression of this gene has significant (p<0.001) association with patient survival are shown in this summary. Whether the prognosis is favourable or unfavourable is indicated in brackets. Each Kaplan-Meier plot is clickable and redirects to a detailed page that includes individual expression and survival data for patients with the selected cancer.
RNA expression overview shows RNA-seq data from The Cancer Genome Atlas (TCGA).
RNA-seq data in 17 cancer types are reported as median FPKM (number Fragments Per Kilobase of exon per Million reads), generated by the The Cancer Genome Atlas (TCGA). RNA cancer tissue category is calculated based on mRNA expression levels across all 17 cancer tissues and include: cancer tissue enriched, cancer group enriched, cancer tissue enhanced, expressed in all, mixed and not detected. To access cancer specific RNA and prognostic data, click on the cancer name.
Antibody staining in 20 different cancers is summarized by a selection of four standard cancer tissue samples representative of the overall staining pattern. From left: colorectal cancer, breast cancer, prostate cancer and lung cancer. An additional fifth image can be added as a complement. The assay and annotation is described here. Note that samples used for immunohistochemistry by the Human Protein Atlas do not correspond to samples in the TCGA dataset.
For each cancer, the fraction of samples with protein expression level high, medium, low, or not detected are provided by the blue-scale color-coding (as described by the color-coding scale in the box to the left). The length of the bar represents the number of patient samples analyzed (max=12 patients). The images and annotations can be accessed by clicking on the cancer name or protein expression bar. If more than one antibody is analyzed, the tabs at the top of the staining summary section can be used to toggle between the different antibodies. The mouse-over function displays additional data for the features in the staining summary view.
Next to the cancer staining data, the protein expression data of normal tissues or specific cell types corresponding to each cancer are shown and protein expression levels are indicated by the blue-scale color coding.
A manually written summary of the overall protein expression pattern across the analyzed cancer tissues.
Cancer tissues showed weak to moderate nuclear staining with additional cytoplasmic and/or membranous positivity in several cases. Rare case of renal and cervical cancer was strongly stained. Majority of the cases of gliomas, lymphomas, melanomas, skin, urothelial, endometrial and prostate cancers were negative.
A manually written summary of the overall protein expression pattern across the analyzed cancer tissues.
Most cancers tissues showed weak to moderate nuclear and cytoplasmic positivity. Testis cancer was negative.
Gene information from Ensembl and Entrez, as well as links to available gene identifiers are displayed here. Information was retrieved from Ensembl if not indicated otherwise.
PSMB9 (HGNC Symbol)
beta1i, LMP2, PSMB6i, RING12
Proteasome subunit beta 9 (HGNC Symbol)
Entrez gene summary
The proteasome is a multicatalytic proteinase complex with a highly ordered ring-shaped 20S core structure. The core structure is composed of 4 rings of 28 non-identical subunits; 2 rings are composed of 7 alpha subunits and 2 rings are composed of 7 beta subunits. Proteasomes are distributed throughout eukaryotic cells at a high concentration and cleave peptides in an ATP/ubiquitin-dependent process in a non-lysosomal pathway. An essential function of a modified proteasome, the immunoproteasome, is the processing of class I MHC peptides. This gene encodes a member of the proteasome B-type family, also known as the T1B family, that is a 20S core beta subunit. This gene is located in the class II region of the MHC (major histocompatibility complex). Expression of this gene is induced by gamma interferon and this gene product replaces catalytic subunit 1 (proteasome beta 6 subunit) in the immunoproteasome. Proteolytic processing is required to generate a mature subunit. [provided by RefSeq, Mar 2010]
The protein browser displays the antigen location on the target protein(s) and the features of the target protein. The tabs at the top of the protein view section can be used to switch between the different splice variants to which an antigen has been mapped.
At the top of the view, the position of the antigen (identified by the corresponding HPA identifier) is shown as a green bar. A yellow triangle on the bar indicates a <100% sequence identity to the protein target.
Under the antigens, the maximum percent sequence identity of the protein to all other proteins from other human genes is displayed, using a sliding window of 10 aa residues (HsID 10) or 50 aa residues (HsID 50) (read more).
If a signal peptide is predicted by a majority of the signal peptide predictors SPOCTOPUS, SignalP 4.0, and Phobius (turquoise) and/or transmembrane regions (orange) are predicted by MDM, these are displayed.
Low complexity regions are shown in yellow and InterPro regions in green. Common (purple) and unique (grey) regions between different splice variants of the gene are also displayed (read more), and at the bottom of the protein view is the protein scale.
The protein information section displays alternative protein-coding transcripts (splice variants) encoded by this gene according to the Ensembl database.
The ENSP identifier links to the Ensembl website protein summary, while the ENST identifier links to the Ensembl website transcript summary for the selected splice variant. The data in the UniProt column can be expanded to show links to all matching UniProt identifiers for this protein.
The protein classes assigned to this protein are shown if expanding the data in the protein class column. Parent protein classes are in bold font and subclasses are listed under the parent class.
The Gene Ontology terms assigned to this protein are listed if expanding the Gene ontology column. The length of the protein (amino acid residues according to Ensembl), molecular mass (kDalton), predicted signal peptide (according to a majority of the signal peptide predictors SPOCTOPUS, SignalP 4.0, and Phobius) and the number of predicted transmembrane region(s) (according to MDM) are also reported.
Enzymes ENZYME proteins Hydrolases Peptidases Threonine-type peptidases Predicted intracellular proteins Plasma proteins FDA approved drug targets Small molecule drugs Protein evidence (Ezkurdia et al 2014)
GO:0000082 [G1/S transition of mitotic cell cycle] GO:0000165 [MAPK cascade] GO:0000186 [activation of MAPKK activity] GO:0000209 [protein polyubiquitination] GO:0000278 [mitotic cell cycle] GO:0000502 [proteasome complex] GO:0001889 [liver development] GO:0002223 [stimulatory C-type lectin receptor signaling pathway] GO:0002474 [antigen processing and presentation of peptide antigen via MHC class I] GO:0002479 [antigen processing and presentation of exogenous peptide antigen via MHC class I, TAP-dependent] GO:0004175 [endopeptidase activity] GO:0004298 [threonine-type endopeptidase activity] GO:0005515 [protein binding] GO:0005654 [nucleoplasm] GO:0005737 [cytoplasm] GO:0005829 [cytosol] GO:0005839 [proteasome core complex] GO:0006521 [regulation of cellular amino acid metabolic process] GO:0006595 [polyamine metabolic process] GO:0006915 [apoptotic process] GO:0006977 [DNA damage response, signal transduction by p53 class mediator resulting in cell cycle arrest] GO:0007173 [epidermal growth factor receptor signaling pathway] GO:0007264 [small GTPase mediated signal transduction] GO:0007265 [Ras protein signal transduction] GO:0007411 [axon guidance] GO:0008286 [insulin receptor signaling pathway] GO:0008543 [fibroblast growth factor receptor signaling pathway] GO:0010467 [gene expression] GO:0010499 [proteasomal ubiquitin-independent protein catabolic process] GO:0012501 [programmed cell death] GO:0014889 [muscle atrophy] GO:0016032 [viral process] GO:0031145 [anaphase-promoting complex-dependent proteasomal ubiquitin-dependent protein catabolic process] GO:0033209 [tumor necrosis factor-mediated signaling pathway] GO:0034641 [cellular nitrogen compound metabolic process] GO:0038061 [NIK/NF-kappaB signaling] GO:0038095 [Fc-epsilon receptor signaling pathway] GO:0042493 [response to drug] GO:0042590 [antigen processing and presentation of exogenous peptide antigen via MHC class I] GO:0042981 [regulation of apoptotic process] GO:0043066 [negative regulation of apoptotic process] GO:0043161 [proteasome-mediated ubiquitin-dependent protein catabolic process] GO:0043279 [response to alkaloid] GO:0043488 [regulation of mRNA stability] GO:0044281 [small molecule metabolic process] GO:0045087 [innate immune response] GO:0048010 [vascular endothelial growth factor receptor signaling pathway] GO:0048011 [neurotrophin TRK receptor signaling pathway] GO:0048536 [spleen development] GO:0048538 [thymus development] GO:0050852 [T cell receptor signaling pathway] GO:0051436 [negative regulation of ubiquitin-protein ligase activity involved in mitotic cell cycle] GO:0051437 [positive regulation of ubiquitin-protein ligase activity involved in regulation of mitotic cell cycle transition] GO:0051439 [regulation of ubiquitin-protein ligase activity involved in mitotic cell cycle] GO:0051603 [proteolysis involved in cellular protein catabolic process] GO:0070062 [extracellular exosome] GO:0070628 [proteasome binding] GO:0071257 [cellular response to electrical stimulus] GO:0071347 [cellular response to interleukin-1] GO:0090090 [negative regulation of canonical Wnt signaling pathway] GO:0090263 [positive regulation of canonical Wnt signaling pathway] GO:0098586 [cellular response to virus] GO:1901423 [response to benzene] GO:1990111 [spermatoproteasome complex]